The linkage among total exchange flow, entrainment, and diffusive salt flux in estuaries is derived analytically using salinity coordinates, revealing the simple but important relationship between total exchange flow and mixing. Mixing is defined and quantified in this paper as the dissipation of salinity variance. The method uses the conservation of volume and salt to quantify and distinguish the diahaline transport of volume (i.e., entrainment) and diahaline diffusive salt flux. A numerical model of the Hudson estuary is used as an example of the application of the method in a realistic estuary with a persistent but temporally variable exchange flow. A notable finding of this analysis is that the total exchange flow and diahaline salt flux are out of phase with respect to the spring–neap cycle. Total exchange flow reaches its maximum near minimum neap tide, but diahaline salt transport reaches its maximum during the maximum spring tide. This phase shift explains the strong temporal variation of stratification and estuarine salt content through the spring–neap cycle. In addition to quantifying temporal variation, the method reveals the spatial variation of total exchange flow, entrainment, and diffusive salt flux through the estuary. For instance, the analysis of the Hudson estuary indicates that diffusive salt flux is intensified in the wider cross sections. The method also provides a simple means of quantifying numerical mixing in ocean models because it provides an estimate of the total dissipation of salinity variance, which is the sum of mixing due to the turbulence closure and numerical mixing.